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Merge branch 'fast-list-append' into 'development' 

Performance improvements when storing/retrieving data from YAML

Closes #180

See merge request damask/DAMASK!561
This commit is contained in:
Martin Diehl 2022-04-20 03:31:10 +00:00
parent 9e2fcfc9df 4a93dbec11
commit dff78154a0
4 changed files with 74 additions and 66 deletions
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2
src/C_routines.c
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@ -88,7 +88,7 @@ void inflate_c(const uLong *s_deflated, const uLong *s_inflated, const Byte defl
#ifdef FYAML
void to_flow_c(char **flow, int* length_flow, const char *mixed){
struct fy_document *fyd = NULL;
enum fy_emitter_cfg_flags emit_flags = FYECF_MODE_FLOW_ONELINE | FYECF_STRIP_LABELS | FYECF_STRIP_DOC;
enum fy_emitter_cfg_flags emit_flags = FYECF_MODE_FLOW_ONELINE | FYECF_STRIP_LABELS | FYECF_STRIP_TAGS |FYECF_STRIP_DOC;
fyd = fy_document_build_from_string(NULL, mixed, -1);
if (!fyd) {

7
src/YAML_parse.f90
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@ -83,7 +83,7 @@ recursive function parse_flow(YAML_flow) result(node)
s, & ! start position of dictionary or list
d ! position of key: value separator (':')
flow_string = trim(adjustl(YAML_flow(:)))
flow_string = trim(adjustl(YAML_flow))
if (len_trim(flow_string) == 0) then
node => emptyDict
return
@ -168,8 +168,11 @@ logical function quotedString(line)
character(len=*), intent(in) :: line
quotedString = .false.
if (len(line) == 0) return
if (scan(line(:1),IO_QUOTES) == 1) then
quotedString = .true.
if(line(len(line):len(line)) /= line(:1)) call IO_error(710,ext_msg=line)
@ -198,7 +201,7 @@ function to_flow(mixed) result(flow)
block
character(len=strlen,kind=c_char), pointer :: s
call c_f_pointer(str_ptr,s)
flow = s
flow = s(:len(s)-1)
end block
call free_C(str_ptr)

19
src/YAML_types.f90
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@ -119,7 +119,8 @@ module YAML_types
type, extends(tNode), public :: tList
class(tItem), pointer :: first => NULL()
class(tItem), pointer :: first => NULL(), &
last => NULL()
contains
procedure :: asFormattedString => tList_asFormattedString
@ -144,7 +145,7 @@ module YAML_types
end type tDict
type :: tItem
type, public :: tItem
character(len=:), allocatable :: key
class(tNode), pointer :: node => NULL()
class(tItem), pointer :: next => NULL()
@ -1348,15 +1349,13 @@ subroutine tList_append(self,node)
type(tItem), pointer :: item
if (.not. associated(self%first)) then
allocate(self%first)
item => self%first
allocate(item)
self%first => item
self%last => item
else
item => self%first
do while (associated(item%next))
item => item%next
enddo
allocate(item%next)
item => item%next
allocate(self%last%next)
item => self%last%next
self%last => item
end if
item%node => node

112
src/material.f90
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@ -91,9 +91,13 @@ subroutine parse()
homogenizations, &
homogenization
class(tItem), pointer :: item
integer, dimension(:), allocatable :: &
counterPhase, &
counterHomogenization
counterHomogenization, &
ho_of
integer, dimension(:,:), allocatable :: ph_of
real(pReal), dimension(:,:), allocatable :: v_of
real(pReal) :: v
integer :: &
@ -102,11 +106,14 @@ subroutine parse()
co, ce, &
ma
materials => config_material%get('material')
phases => config_material%get('phase')
homogenizations => config_material%get('homogenization')
call sanityCheck(materials, homogenizations)
if (maxval(discretization_materialAt) > materials%length) &
call IO_error(155,ext_msg='More materials requested than found in material.yaml')
#if defined (__GFORTRAN__)
material_name_phase = getKeys(phases)
@ -123,6 +130,49 @@ subroutine parse()
end do
homogenization_maxNconstituents = maxval(homogenization_Nconstituents)
allocate(material_v(homogenization_maxNconstituents,discretization_Ncells),source=0.0_pReal)
allocate(material_O_0(materials%length))
allocate(material_F_i_0(materials%length))
allocate(ho_of(materials%length))
allocate(ph_of(materials%length,homogenization_maxNconstituents),source=-1)
allocate( v_of(materials%length,homogenization_maxNconstituents),source=0.0_pReal)
! parse YAML structure
select type(materials)
class is(tList)
item => materials%first
do ma = 1, materials%length
material => item%node
ho_of(ma) = homogenizations%getIndex(material%get_asString('homogenization'))
constituents => material%get('constituents')
homogenization => homogenizations%get(ho_of(ma))
if (constituents%length /= homogenization%get_asInt('N_constituents')) call IO_error(148)
allocate(material_O_0(ma)%data(constituents%length))
allocate(material_F_i_0(ma)%data(1:3,1:3,constituents%length))
do co = 1, constituents%length
constituent => constituents%get(co)
v_of(ma,co) = constituent%get_asFloat('v')
ph_of(ma,co) = phases%getIndex(constituent%get_asString('phase'))
call material_O_0(ma)%data(co)%fromQuaternion(constituent%get_as1dFloat('O',requiredSize=4))
material_F_i_0(ma)%data(1:3,1:3,co) = constituent%get_as2dFloat('F_i',defaultVal=math_I3,requiredShape=[3,3])
end do
if (dNeq(sum(v_of(ma,:)),1.0_pReal,1.e-9_pReal)) call IO_error(153,ext_msg='constituent')
item => item%next
end do
end select
allocate(counterPhase(phases%length),source=0)
allocate(counterHomogenization(homogenizations%length),source=0)
@ -132,12 +182,13 @@ subroutine parse()
allocate(material_phaseID(homogenization_maxNconstituents,discretization_Ncells),source=0)
allocate(material_phaseEntry(homogenization_maxNconstituents,discretization_Ncells),source=0)
allocate(material_v(homogenization_maxNconstituents,discretization_Ncells),source=0.0_pReal)
! build mappings
do el = 1, discretization_Nelems
material => materials%get(discretization_materialAt(el))
ho = homogenizations%getIndex(material%get_asString('homogenization'))
ma = discretization_materialAt(el)
ho = ho_of(ma)
do ip = 1, discretization_nIPs
ce = (el-1)*discretization_nIPs + ip
material_homogenizationID(ce) = ho
@ -145,13 +196,11 @@ subroutine parse()
material_homogenizationEntry(ce) = counterHomogenization(ho)
end do
constituents => material%get('constituents')
do co = 1, constituents%length
constituent => constituents%get(co)
do co = 1, size(ph_of(ma,:)>0)
v = constituent%get_asFloat('v')
v = v_of(ma,co)
ph = ph_of(ma,co)
ph = phases%getIndex(constituent%get_asString('phase'))
do ip = 1, discretization_nIPs
ce = (el-1)*discretization_nIPs + ip
material_phaseID(co,ce) = ph
@ -161,54 +210,11 @@ subroutine parse()
end do
end do
if (dNeq(sum(material_v(1:constituents%length,ce)),1.0_pReal,1.e-9_pReal)) &
call IO_error(153,ext_msg='constituent')
end do
allocate(material_O_0(materials%length))
allocate(material_F_i_0(materials%length))
do ma = 1, materials%length
material => materials%get(ma)
constituents => material%get('constituents')
allocate(material_O_0(ma)%data(constituents%length))
allocate(material_F_i_0(ma)%data(1:3,1:3,constituents%length))
do co = 1, constituents%length
constituent => constituents%get(co)
call material_O_0(ma)%data(co)%fromQuaternion(constituent%get_as1dFloat('O',requiredSize=4))
material_F_i_0(ma)%data(1:3,1:3,co) = constituent%get_as2dFloat('F_i',defaultVal=math_I3,requiredShape=[3,3])
enddo
enddo
end subroutine parse
!--------------------------------------------------------------------------------------------------
!> @brief Check if material.yaml is consistent and contains sufficient # of materials
!--------------------------------------------------------------------------------------------------
subroutine sanityCheck(materials,homogenizations)
class(tNode), intent(in) :: materials, &
homogenizations
class(tNode), pointer :: material, &
homogenization, &
constituents
integer :: m
if (maxval(discretization_materialAt) > materials%length) &
call IO_error(155,ext_msg='More materials requested than found in material.yaml')
do m = 1, materials%length
material => materials%get(m)
constituents => material%get('constituents')
homogenization => homogenizations%get(material%get_asString('homogenization'))
if (constituents%length /= homogenization%get_asInt('N_constituents')) call IO_error(148)
end do
end subroutine sanityCheck
#if defined (__GFORTRAN__)
!--------------------------------------------------------------------------------------------------
!> @brief %keys() is broken on gfortran